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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2022-02-17, 22:15 based on data in:

        General Statistics

        Showing 210/210 rows and 4/5 columns.
        Sample Name% Dups% GCLengthM Seqs
        GB64_2_B2G1_2011_R1_val_1
        18.6%
        24%
        126 bp
        26.9
        GB64_2_B2G1_2011_R2_val_2
        17.5%
        24%
        110 bp
        26.9
        GC03_2_B3G1_2012_R1_val_1
        22.1%
        24%
        126 bp
        27.7
        GC03_2_B3G1_2012_R2_val_2
        21.3%
        24%
        110 bp
        27.7
        GF36_2_B1G2_2011_R1_val_1
        16.9%
        23%
        125 bp
        26.3
        GF36_2_B1G2_2011_R2_val_2
        16.3%
        23%
        110 bp
        26.3
        GG45_1_B4G0_2012_R1_val_1
        18.8%
        24%
        125 bp
        22.5
        GG45_1_B4G0_2012_R2_val_2
        17.8%
        24%
        110 bp
        22.5
        GS17_2_B1G2_2011_R1_val_1
        19.5%
        23%
        127 bp
        27.5
        GS17_2_B1G2_2011_R2_val_2
        18.6%
        23%
        111 bp
        27.5
        GY02_1_B1G1_2010_R1_val_1
        36.9%
        26%
        124 bp
        25.4
        GY02_1_B1G1_2010_R2_val_2
        35.7%
        26%
        109 bp
        25.4
        GY19_2_B2G2_2012_R1_val_1
        21.3%
        24%
        125 bp
        27.1
        GY19_2_B2G2_2012_R2_val_2
        20.4%
        24%
        110 bp
        27.1
        OA22_2_B4G2_2014_R1_val_1
        17.0%
        23%
        126 bp
        23.6
        OA22_2_B4G2_2014_R2_val_2
        16.4%
        23%
        110 bp
        23.6
        OB07_1_B4G2_2014_R1_val_1
        17.6%
        24%
        125 bp
        22.0
        OB07_1_B4G2_2014_R2_val_2
        16.6%
        24%
        110 bp
        22.0
        OB21_1_B3G3_2014_R1_val_1
        19.0%
        24%
        126 bp
        23.2
        OB21_1_B3G3_2014_R2_val_2
        18.1%
        24%
        110 bp
        23.2
        OB32_2_B4G1_2013_R1_val_1
        20.7%
        24%
        126 bp
        26.0
        OB32_2_B4G1_2013_R2_val_2
        19.6%
        23%
        110 bp
        26.0
        OB40_1_B3G3_2014_R1_val_1
        20.8%
        24%
        126 bp
        26.2
        OB40_1_B3G3_2014_R2_val_2
        19.5%
        24%
        110 bp
        26.2
        OC00_1_B5G3_2018_R1_val_1
        18.9%
        23%
        125 bp
        24.0
        OC00_1_B5G3_2018_R2_val_2
        17.9%
        23%
        110 bp
        24.0
        OC14_2_B1G1_2010_R1_val_1
        17.4%
        23%
        126 bp
        26.5
        OC14_2_B1G1_2010_R2_val_2
        16.7%
        23%
        110 bp
        26.5
        OD00_1_B1G3_2012_R1_val_1
        18.2%
        24%
        125 bp
        21.8
        OD00_1_B1G3_2012_R2_val_2
        17.2%
        24%
        110 bp
        21.8
        OD08_2_B1G3_2012_R1_val_1
        17.6%
        23%
        126 bp
        27.0
        OD08_2_B1G3_2012_R2_val_2
        16.7%
        23%
        110 bp
        27.0
        OD23_1_B5G2_2017_R1_val_1
        17.9%
        23%
        126 bp
        25.8
        OD23_1_B5G2_2017_R2_val_2
        16.8%
        23%
        110 bp
        25.8
        OD35_2_B4G2_2014_R1_val_1
        19.8%
        24%
        126 bp
        23.1
        OD35_2_B4G2_2014_R2_val_2
        18.7%
        24%
        110 bp
        23.1
        OD66_2_B4G2_2014_R1_val_1
        17.8%
        24%
        126 bp
        24.6
        OD66_2_B4G2_2014_R2_val_2
        16.8%
        24%
        110 bp
        24.6
        OF00_1_B4G1_2013_R1_val_1
        18.5%
        23%
        125 bp
        27.1
        OF00_1_B4G1_2013_R2_val_2
        17.6%
        23%
        110 bp
        27.1
        OF01_1_B5G0_2015_R1_val_1
        17.6%
        24%
        126 bp
        21.5
        OF01_1_B5G0_2015_R2_val_2
        16.7%
        24%
        110 bp
        21.5
        OF14_2_B1G3_2012_R1_val_1
        27.9%
        26%
        125 bp
        23.2
        OF14_2_B1G3_2012_R2_val_2
        26.7%
        26%
        109 bp
        23.2
        OF15_2_B1G3_2012_R1_val_1
        23.4%
        24%
        123 bp
        26.1
        OF15_2_B1G3_2012_R2_val_2
        22.7%
        24%
        108 bp
        26.1
        OG27_1_B5G0_2015_R1_val_1
        18.4%
        23%
        126 bp
        26.4
        OG27_1_B5G0_2015_R2_val_2
        17.6%
        23%
        110 bp
        26.4
        OH01_1_B4G3_2015_R1_val_1
        17.0%
        23%
        125 bp
        26.9
        OH01_1_B4G3_2015_R2_val_2
        16.4%
        23%
        110 bp
        26.9
        OH11_1_B4G3_2015_R1_val_1
        18.0%
        24%
        126 bp
        26.6
        OH11_1_B4G3_2015_R2_val_2
        17.0%
        24%
        110 bp
        26.6
        OH46_1_B3G0_2011_R1_val_1
        18.3%
        23%
        126 bp
        23.6
        OH46_1_B3G0_2011_R2_val_2
        17.1%
        23%
        110 bp
        23.6
        OI00_1_B1G2_2011_R1_val_1
        18.9%
        23%
        126 bp
        27.0
        OI00_1_B1G2_2011_R2_val_2
        17.9%
        23%
        110 bp
        27.0
        OK00_1_B5G0_2015_R1_val_1
        16.6%
        23%
        126 bp
        26.7
        OK00_1_B5G0_2015_R2_val_2
        15.9%
        23%
        110 bp
        26.7
        OK13_2_B4G3_2015_R1_val_1
        17.9%
        23%
        126 bp
        27.1
        OK13_2_B4G3_2015_R2_val_2
        16.9%
        23%
        110 bp
        27.1
        OK15_2_B4G3_2015_R1_val_1
        16.7%
        23%
        126 bp
        26.5
        OK15_2_B4G3_2015_R2_val_2
        15.9%
        23%
        110 bp
        26.5
        ON56_2_2_B1G2_2011_R1_val_1
        18.1%
        23%
        124 bp
        23.0
        ON56_2_2_B1G2_2011_R2_val_2
        17.3%
        23%
        108 bp
        23.0
        ON56_2_B1G2_2011_R1_val_1
        17.3%
        23%
        125 bp
        26.4
        ON56_2_B1G2_2011_R2_val_2
        16.5%
        23%
        110 bp
        26.4
        OP04_1_B2G2_2012_R1_val_1
        17.7%
        24%
        125 bp
        21.0
        OP04_1_B2G2_2012_R2_val_2
        16.8%
        24%
        109 bp
        21.0
        OP19_1_B2G1_2011_R1_val_1
        17.1%
        23%
        124 bp
        26.6
        OP19_1_B2G1_2011_R2_val_2
        16.5%
        23%
        109 bp
        26.6
        OP21_1_B4G0_2012_R1_val_1
        18.7%
        24%
        126 bp
        25.3
        OP21_1_B4G0_2012_R2_val_2
        17.6%
        24%
        110 bp
        25.3
        OP49_1_B1G1_2010_R1_val_1
        17.7%
        23%
        126 bp
        25.9
        OP49_1_B1G1_2010_R2_val_2
        16.9%
        23%
        110 bp
        25.9
        OR05_1_B4G3_2015_R1_val_1
        18.2%
        24%
        126 bp
        24.0
        OR05_1_B4G3_2015_R2_val_2
        17.1%
        24%
        110 bp
        24.0
        OR29_1_B4G3_2015_R1_val_1
        17.7%
        24%
        126 bp
        25.5
        OR29_1_B4G3_2015_R2_val_2
        16.6%
        24%
        110 bp
        25.5
        OS03_1_B1G2_2011_R1_val_1
        18.1%
        23%
        126 bp
        25.8
        OS03_1_B1G2_2011_R2_val_2
        17.4%
        23%
        110 bp
        25.8
        OS06_1_B4G0_2012_R1_val_1
        20.1%
        24%
        125 bp
        23.7
        OS06_1_B4G0_2012_R2_val_2
        19.2%
        24%
        109 bp
        23.7
        OS41_2_B2G1_2011_R1_val_1
        16.9%
        23%
        125 bp
        26.8
        OS41_2_B2G1_2011_R2_val_2
        16.0%
        23%
        110 bp
        26.8
        OU11_2_B2G2_2012_R1_val_1
        18.4%
        24%
        126 bp
        24.5
        OU11_2_B2G2_2012_R2_val_2
        17.3%
        24%
        110 bp
        24.5
        OU20_1_B2G1_2011_R1_val_1
        20.9%
        23%
        123 bp
        26.6
        OU20_1_B2G1_2011_R2_val_2
        20.1%
        23%
        108 bp
        26.6
        OV01_2_B4G1_2013_R1_val_1
        18.2%
        24%
        125 bp
        26.4
        OV01_2_B4G1_2013_R2_val_2
        17.2%
        24%
        110 bp
        26.4
        OZ04_1_B2G2_2012_R1_val_1
        18.1%
        23%
        126 bp
        25.0
        OZ04_1_B2G2_2012_R2_val_2
        17.5%
        23%
        111 bp
        25.0
        RA09_1_B2G0_2010_R1_val_1
        21.3%
        24%
        126 bp
        27.1
        RA09_1_B2G0_2010_R2_val_2
        19.9%
        24%
        110 bp
        27.1
        RA12_2_B2G0_2010_R1_val_1
        18.8%
        24%
        126 bp
        29.2
        RA12_2_B2G0_2010_R2_val_2
        17.9%
        24%
        111 bp
        29.2
        RA17_1_B2G0_2010_R1_val_1
        16.5%
        23%
        126 bp
        25.5
        RA17_1_B2G0_2010_R2_val_2
        15.8%
        23%
        110 bp
        25.5
        RA47_2_B2G0_2010_R1_val_1
        18.6%
        24%
        126 bp
        26.3
        RA47_2_B2G0_2010_R2_val_2
        17.6%
        24%
        110 bp
        26.3
        RA49_1_B2G0_2010_R1_val_1
        16.2%
        23%
        126 bp
        25.9
        RA49_1_B2G0_2010_R2_val_2
        15.3%
        23%
        111 bp
        25.9
        RA52_2_B2G0_2010_R1_val_1
        19.7%
        24%
        126 bp
        27.3
        RA52_2_B2G0_2010_R2_val_2
        18.9%
        24%
        111 bp
        27.3
        RB34_2_B3G0_2011_R1_val_1
        18.2%
        24%
        126 bp
        26.7
        RB34_2_B3G0_2011_R2_val_2
        17.4%
        24%
        110 bp
        26.7
        RB38_2_B4G0_2012_R1_val_1
        20.7%
        24%
        126 bp
        28.0
        RB38_2_B4G0_2012_R2_val_2
        19.6%
        24%
        110 bp
        28.0
        RB55_2_B4G0_2012_R1_val_1
        16.4%
        23%
        126 bp
        26.4
        RB55_2_B4G0_2012_R2_val_2
        15.8%
        23%
        111 bp
        26.4
        RB66_2_B4G0_2012_R1_val_1
        20.6%
        24%
        125 bp
        27.1
        RB66_2_B4G0_2012_R2_val_2
        19.6%
        24%
        110 bp
        27.1
        RW43_1_B1G0_2009_R1_val_1
        19.3%
        24%
        126 bp
        26.9
        RW43_1_B1G0_2009_R2_val_2
        18.3%
        24%
        110 bp
        26.9
        RW79_2_B1G0_2009_R1_val_1
        17.9%
        24%
        126 bp
        26.7
        RW79_2_B1G0_2009_R2_val_2
        16.5%
        24%
        110 bp
        26.7
        RW91_2_B1G0_2009_R1_val_1
        23.8%
        24%
        126 bp
        26.3
        RW91_2_B1G0_2009_R2_val_2
        22.6%
        24%
        110 bp
        26.3
        RX15_2_B5G0_2015_R1_val_1
        17.7%
        23%
        126 bp
        26.7
        RX15_2_B5G0_2015_R2_val_2
        16.6%
        24%
        110 bp
        26.7
        RX25_1_B4G2_2014_R1_val_1
        17.9%
        23%
        126 bp
        24.4
        RX25_1_B4G2_2014_R2_val_2
        16.8%
        23%
        110 bp
        24.4
        RX28_1_B5G1_2016_R1_val_1
        17.3%
        23%
        126 bp
        24.8
        RX28_1_B5G1_2016_R2_val_2
        16.6%
        23%
        110 bp
        24.8
        RX38_2_B5G0_2015_R1_val_1
        18.3%
        23%
        126 bp
        25.9
        RX38_2_B5G0_2015_R2_val_2
        17.3%
        24%
        110 bp
        25.9
        RX43_1_B4G1_2013_R1_val_1
        19.3%
        23%
        126 bp
        27.1
        RX43_1_B4G1_2013_R2_val_2
        18.3%
        23%
        110 bp
        27.1
        RX81_2_B5G0_2015_R1_val_1
        16.9%
        23%
        125 bp
        27.5
        RX81_2_B5G0_2015_R2_val_2
        16.0%
        23%
        110 bp
        27.5
        YA15_2_B5G3_2018_R1_val_1
        19.3%
        23%
        125 bp
        27.6
        YA15_2_B5G3_2018_R2_val_2
        18.2%
        23%
        109 bp
        27.6
        YB41_1_B3G2_2013_R1_val_1
        20.4%
        31%
        125 bp
        27.5
        YB41_1_B3G2_2013_R2_val_2
        19.2%
        31%
        109 bp
        27.5
        YB82_1_B4G2_2014_R1_val_1
        18.0%
        24%
        126 bp
        26.6
        YB82_1_B4G2_2014_R2_val_2
        17.3%
        24%
        111 bp
        26.6
        YC01_1_B2G3_2013_R1_val_1
        18.6%
        24%
        126 bp
        27.1
        YC01_1_B2G3_2013_R2_val_2
        17.6%
        23%
        110 bp
        27.1
        YC06_1_B1G3_2012_R1_val_1
        20.2%
        24%
        126 bp
        27.9
        YC06_1_B1G3_2012_R2_val_2
        19.3%
        24%
        110 bp
        27.9
        YC32_2_B1G3_2012_R1_val_1
        16.5%
        26%
        126 bp
        24.6
        YC32_2_B1G3_2012_R2_val_2
        15.7%
        26%
        110 bp
        24.6
        YC36_2_B2G3_2013_R1_val_1
        19.9%
        23%
        126 bp
        24.5
        YC36_2_B2G3_2013_R2_val_2
        19.0%
        23%
        110 bp
        24.5
        YC94_1_B5G3_2018_R1_val_1
        18.9%
        23%
        126 bp
        26.9
        YC94_1_B5G3_2018_R2_val_2
        18.2%
        23%
        110 bp
        26.9
        YD08_2_B2G3_2013_R1_val_1
        18.4%
        24%
        126 bp
        27.7
        YD08_2_B2G3_2013_R2_val_2
        17.4%
        24%
        110 bp
        27.7
        YD12_1_B2G3_2013_R1_val_1
        19.0%
        24%
        126 bp
        24.0
        YD12_1_B2G3_2013_R2_val_2
        18.4%
        23%
        110 bp
        24.0
        YD41_1_B5G2_2017_R1_val_1
        19.4%
        24%
        126 bp
        22.6
        YD41_1_B5G2_2017_R2_val_2
        18.7%
        24%
        110 bp
        22.6
        YF03_1_B3G1_2012_R1_val_1
        17.6%
        23%
        126 bp
        24.1
        YF03_1_B3G1_2012_R2_val_2
        16.9%
        23%
        110 bp
        24.1
        YF21_1_B5G1_2016_R1_val_1
        18.6%
        23%
        126 bp
        26.3
        YF21_1_B5G1_2016_R2_val_2
        17.9%
        23%
        110 bp
        26.3
        YF39_2_B1G1_2010_R1_val_1
        22.3%
        24%
        126 bp
        27.3
        YF39_2_B1G1_2010_R2_val_2
        21.4%
        24%
        110 bp
        27.3
        YF42_2_B1G1_2010_R1_val_1
        18.9%
        24%
        126 bp
        27.5
        YF42_2_B1G1_2010_R2_val_2
        17.8%
        24%
        110 bp
        27.5
        YF50_2_B5G2_2017_R1_val_1
        17.9%
        23%
        126 bp
        26.7
        YF50_2_B5G2_2017_R2_val_2
        17.1%
        23%
        110 bp
        26.7
        YH10_2_B5G2_2017_R1_val_1
        16.1%
        23%
        125 bp
        27.1
        YH10_2_B5G2_2017_R2_val_2
        15.3%
        23%
        110 bp
        27.1
        YI03_1_B5G2_2017_R1_val_1
        18.8%
        24%
        126 bp
        25.7
        YI03_1_B5G2_2017_R2_val_2
        16.8%
        24%
        109 bp
        25.7
        YI22_1_B2G3_2013_R1_val_1
        18.7%
        23%
        126 bp
        27.1
        YI22_1_B2G3_2013_R2_val_2
        17.7%
        23%
        110 bp
        27.1
        YI32_2_B2G3_2013_R1_val_1
        20.2%
        24%
        126 bp
        27.6
        YI32_2_B2G3_2013_R2_val_2
        19.4%
        23%
        111 bp
        27.6
        YK54_2_B5G1_2016_R1_val_1
        18.3%
        24%
        125 bp
        26.9
        YK54_2_B5G1_2016_R2_val_2
        17.4%
        24%
        110 bp
        26.9
        YK67_2_B3G2_2013_R1_val_1
        19.7%
        23%
        126 bp
        26.5
        YK67_2_B3G2_2013_R2_val_2
        18.9%
        23%
        111 bp
        26.5
        YL51_2_B4G2_2014_R1_val_1
        18.1%
        23%
        126 bp
        26.0
        YL51_2_B4G2_2014_R2_val_2
        17.4%
        23%
        110 bp
        26.0
        YN39_1_B1G0_2009_R1_val_1
        16.4%
        26%
        125 bp
        25.5
        YN39_1_B1G0_2009_R2_val_2
        15.7%
        26%
        110 bp
        25.5
        YP02_1_B5G1_2016_R1_val_1
        18.4%
        23%
        125 bp
        21.5
        YP02_1_B5G1_2016_R2_val_2
        17.4%
        23%
        110 bp
        21.5
        YP34_1_B4G1_2013_R1_val_1
        19.6%
        24%
        126 bp
        24.9
        YP34_1_B4G1_2013_R2_val_2
        18.8%
        24%
        110 bp
        24.9
        YP50_1_B4G2_2014_R1_val_1
        19.0%
        23%
        126 bp
        26.7
        YP50_1_B4G2_2014_R2_val_2
        17.3%
        24%
        109 bp
        26.7
        YP51_2_B5G1_2016_R1_val_1
        18.3%
        23%
        125 bp
        24.1
        YP51_2_B5G1_2016_R2_val_2
        17.5%
        23%
        109 bp
        24.1
        YR06_1_B1G2_2011_R1_val_1
        16.9%
        23%
        126 bp
        26.8
        YR06_1_B1G2_2011_R2_val_2
        16.2%
        23%
        110 bp
        26.8
        YR58_2_B5G1_2016_R1_val_1
        16.8%
        23%
        126 bp
        24.8
        YR58_2_B5G1_2016_R2_val_2
        15.9%
        23%
        110 bp
        24.8
        YR66_2_B5G2_2017_R1_val_1
        18.5%
        24%
        126 bp
        27.3
        YR66_2_B5G2_2017_R2_val_2
        17.7%
        23%
        110 bp
        27.3
        YS03_1_B5G3_2018_R1_val_1
        18.2%
        24%
        126 bp
        22.1
        YS03_1_B5G3_2018_R2_val_2
        17.4%
        24%
        110 bp
        22.1
        YS63_1_B5G3_2018_R1_val_1
        17.1%
        23%
        126 bp
        23.8
        YS63_1_B5G3_2018_R2_val_2
        16.4%
        23%
        110 bp
        23.8
        YT07_2_B4G1_2013_R1_val_1
        18.4%
        23%
        126 bp
        22.8
        YT07_2_B4G1_2013_R2_val_2
        17.4%
        23%
        110 bp
        22.8
        YT25_2_B4G3_2015_R1_val_1
        18.8%
        23%
        125 bp
        25.3
        YT25_2_B4G3_2015_R2_val_2
        17.8%
        23%
        110 bp
        25.3
        YT33_2_B4G3_2015_R1_val_1
        18.7%
        23%
        126 bp
        26.0
        YT33_2_B4G3_2015_R2_val_2
        17.6%
        24%
        110 bp
        26.0
        YT54_1_B1G1_2010_R1_val_1
        18.3%
        24%
        126 bp
        26.7
        YT54_1_B1G1_2010_R2_val_2
        17.4%
        24%
        110 bp
        26.7
        YV33_2_B2G2_2012_R1_val_1
        21.0%
        23%
        125 bp
        24.5
        YV33_2_B2G2_2012_R2_val_2
        20.0%
        23%
        109 bp
        24.5
        YY01_1_B2G1_2011_R1_val_1
        17.2%
        23%
        125 bp
        26.3
        YY01_1_B2G1_2011_R2_val_2
        16.2%
        23%
        110 bp
        26.3
        YY17_2_B2G1_2011_R1_val_1
        19.3%
        23%
        126 bp
        27.7
        YY17_2_B2G1_2011_R2_val_2
        18.5%
        23%
        110 bp
        27.7

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        210 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        loading..

        MultiQC v1.9 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.